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- EMDB-54377: Heterodimeric ABC exporter TmrAB (EQ mutant) in ATP-bound outward... -

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Basic information

Entry
Database: EMDB / ID: EMD-54377
TitleHeterodimeric ABC exporter TmrAB (EQ mutant) in ATP-bound outward-facing occluded conformation in the absence of Mg2+
Map data
Sample
  • Complex: Heterodimeric ABC exporter TmrAB (EQ mutant) in ATP-bound outward-facing occluded conformation in the absence of Mg2+
    • Protein or peptide: Multidrug resistance ABC transporter ATP-binding and permease protein
    • Protein or peptide: Multidrug resistance ABC transporter ATP-binding and permease protein
    • Protein or peptide: Nanobody Nb9F10
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordsatp-binding cassette protein / ABC transporter / membrane protein / heterodimer / exporter / transport protein / ATPase
Function / homology
Function and homology information


ABC-type oligopeptide transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Multidrug resistance ABC transporter ATP-binding and permease protein / Multidrug resistance ABC transporter ATP-binding and permease protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsSusac L / Nocker C / Tampe R
Funding support Germany, European Union, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC1507/Z02 Germany
German Research Foundation (DFG)CRC1507/P18 Germany
European Research Council (ERC)789121European Union
European Research Council (ERC)101141396European Union
CitationJournal: Nat Commun / Year: 2026
Title: Single-molecule dynamics reveal ATP binding alone powers substrate translocation by an ABC transporter.
Authors: Christoph Nocker / Matija Pečak / Tobias Nocker / Amin Fahim / Lukas Sušac / Robert Tampé /
Abstract: ATP-binding cassette (ABC) transporters are molecular machines involved in diverse physiological processes, including antigen processing by TAP, a key component of adaptive immunity. TAP and its ...ATP-binding cassette (ABC) transporters are molecular machines involved in diverse physiological processes, including antigen processing by TAP, a key component of adaptive immunity. TAP and its bacterial homolog TmrAB use ATP to translocate peptides across membranes, yet the precise mechanism linking ATP binding to substrate movement remains unclear. Here, we employ a single-molecule FRET sensor to visualize single translocation events by individual ABC transporters and thereby overcome the limitations of ensemble averaging. This approach reveals that substrate transport is driven by a conformational switch from the inward- to the outward-facing state. Using a slow-turnover TmrAB variant, we demonstrate that ATP binding alone, even in the absence of Mg, is sufficient to drive a single round of peptide translocation. Cryo-EM structures of wild-type and slow-turnover TmrAB show that ATP binding induces the outward-facing conformation even without Mg. In wild-type TmrAB, this conformational transition supports a single translocation event, whereas Mg-dependent ATP hydrolysis is required to reset the transporter. These findings establish a direct mechanistic link between ATP binding and substrate translocation at single-molecule resolution and provide insight into the catalytic cycle of ABC transporters.
History
DepositionJul 15, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54377.png

Downloads & links

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Map

FileDownload / File: emd_54377.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.0391686 - 1.7181928
Average (Standard dev.)-0.0015513296 (±0.034900106)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 285.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54377_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54377_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Heterodimeric ABC exporter TmrAB (EQ mutant) in ATP-bound outward...

EntireName: Heterodimeric ABC exporter TmrAB (EQ mutant) in ATP-bound outward-facing occluded conformation in the absence of Mg2+
Components
  • Complex: Heterodimeric ABC exporter TmrAB (EQ mutant) in ATP-bound outward-facing occluded conformation in the absence of Mg2+
    • Protein or peptide: Multidrug resistance ABC transporter ATP-binding and permease protein
    • Protein or peptide: Multidrug resistance ABC transporter ATP-binding and permease protein
    • Protein or peptide: Nanobody Nb9F10
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Heterodimeric ABC exporter TmrAB (EQ mutant) in ATP-bound outward...

SupramoleculeName: Heterodimeric ABC exporter TmrAB (EQ mutant) in ATP-bound outward-facing occluded conformation in the absence of Mg2+
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Thermus thermophilus (bacteria)

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Macromolecule #1: Multidrug resistance ABC transporter ATP-binding and permease protein

MacromoleculeName: Multidrug resistance ABC transporter ATP-binding and permease protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 70.663805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTEDTYSKAF DRALFARILR YVWPYRLQVV LALLFLLVVT LAAAATPLFF KWAIDLALVP TEPRPLAERF HLLLWISLGF LAVRAVHFA ATYGETYLIQ WVGQRVLFDL RSDLFAKLMR LHPGFYDRNP VGRLMTRVTS DVDAINQFIT GGLVGVIADL F TLVGLLGF ...String:
MTEDTYSKAF DRALFARILR YVWPYRLQVV LALLFLLVVT LAAAATPLFF KWAIDLALVP TEPRPLAERF HLLLWISLGF LAVRAVHFA ATYGETYLIQ WVGQRVLFDL RSDLFAKLMR LHPGFYDRNP VGRLMTRVTS DVDAINQFIT GGLVGVIADL F TLVGLLGF MLFLSPKLTL VVLLVAPVLL AVTTWVRLGM RSAYREMRLR LARVNAALQE NLSGVETIQL FVKEREREEK FD RLNRDLF RAWVEIIRWF ALFFPVVGFL GDFAVASLVY YGGGEVVRGA VSLGLLVAFV DYTRQLFQPL QDLSDKFNLF QGA MASAER IFGVLDTEEE LKDPEDPTPI RGFRGEVEFR DVWLAYTPKG VEPTEKDWVL KGVSFRVRPG EKVALVGATG AGKT SVVSL IARFYDPQRG CVFLDGVDVR RYRQEELRRH VGIVLQEPFL FSGTVLDNLR LFDPSVPPER VEEVARFLGA HEFIL RLPK GYQTVLGERG AGLSTGEKQL LALVRALLAS PDILLILDQA TASVDSETEK RLQEALYKAM EGRTSLIIAH RLSTIR HVD RILVFRKGRL VEEGSHEELL AKGGYYAALY RLQFQEAKLG GGGENLYFQG HHHHHHHHHH

UniProtKB: Multidrug resistance ABC transporter ATP-binding and permease protein

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Macromolecule #2: Multidrug resistance ABC transporter ATP-binding and permease protein

MacromoleculeName: Multidrug resistance ABC transporter ATP-binding and permease protein
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 64.634457 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTGRSAAPLL RRLWPYVGRY RWRYLWAVLA GLVSIFFFVL TPYFLRLAVD AVQAGRGFGV YALAIVASAA LSGLLSYAMR RLAVVASRQ VEYDLRRDLL HHLLTLDRDF YHKHRVGDLM NRLNTDLSAV REMVGPGILM GSRLSFLVLL AFLSMYAVNA R LAFYLTLI ...String:
MTGRSAAPLL RRLWPYVGRY RWRYLWAVLA GLVSIFFFVL TPYFLRLAVD AVQAGRGFGV YALAIVASAA LSGLLSYAMR RLAVVASRQ VEYDLRRDLL HHLLTLDRDF YHKHRVGDLM NRLNTDLSAV REMVGPGILM GSRLSFLVLL AFLSMYAVNA R LAFYLTLI LPGIFLAMRF LLRLIDRRYR EAQEVFDRIS TLAQEAFSGI RVVKGYALER RMVAWFQDLN RLYVEKSLAL AR VEGPLHA LLGFLMGFAF LTVLWAGGAM VVRGELSVGE LVQFNAYLAQ LTWPILGLGW VMALYQRGLT SLRRLFELLD EKP AIRDED PLPLALEDLS GEVRFEGVGL KRDGRWLLRG LTLTIPEGMT LGITGRTGSG KSLLAALVPR LLDPSEGRVY VGGH EARRI PLAVLRKAVG VAPQEPFLFS ETILENIAFG LDEVDRERVE WAARLAGIHE EILAFPKGYE TVLGERGITL SGGQR QRVA LARALAKRPK ILILDDALSA VDAETEARIL QGLKTVLGKQ TTLLISHRTA ALRHADWIIV LDGGRIVEEG THESLL QAG GLYAEMDRLQ KEVEA

UniProtKB: Multidrug resistance ABC transporter ATP-binding and permease protein

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Macromolecule #3: Nanobody Nb9F10

MacromoleculeName: Nanobody Nb9F10 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 14.594405 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAQLQLVESG GGLVQPGDSL RLSCAVSGSA LDYNAIGWFR QAPGKEREGV ACISKITGNT AYADSVKGRF TISRDNAKNT VHLQMNSLK PEDTAVYYCA TVTAVLLPGR CVPGKYWGQG TPVTVSSHHH HHHEPEA

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 28.3 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 226815
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6rai


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9rye:
Heterodimeric ABC exporter TmrAB (EQ mutant) in ATP-bound outward-facing occluded conformation in the absence of Mg2+

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